Unravelling the Probiotic and Safety Profile of Lactiplantibacillus plantarum 022AE: A Multi-Omics Approach Integrating Genomics and Phenotypic Data

Introduction Lactiplantibacillus plantarum is one of the most varied species of lactic acid bacteria in various environments. Probiotics are beneficial organisms that help balance the gut microbiome and promote general health. The purpose of this study was to perform preliminary phenotypic and genetic characterization of the probiotic strain L. plantarum 022AE. Method Using hybrid assembly, L. plantarum 022AE was sequenced, producing a 3.23 Mb scaffold. Using NCBI-BLASTN, the strain's identification was verified. Genome annotation was used to evaluate safety characteristics. In vitro tests were employed to assess cytotoxicity, antibacterial activity, bile acid tolerance, epithelial adhesion, surface characteristics, cell lining to verify in vivo adhesion, and antibiotic susceptibility (CLSI). Genes associated with virulence, adhesion, and stress survival were discovered by comparative genomics. The safety and probiotic qualities of L. plantarum 022AE were shown to be favourable by full-genome analysis and phenotypic assessment. Results For complete genome sequencing of L. plantarum 022AE, a single scaffold of 3,234,271 bp was obtained via hybrid assembly. NCBI-BLASTN tools analysis showed L. plantarum 022AE to be 100% identical to the reference strain HAC01. Gene annotation and downstream analysis revealed safety attributes, like absence of transferable antibiotic resistance genes, virulence factor genes, active biogenic amine-producing genes, enterotoxin genes, emetic toxin genes, and prophage sequences. In vitro phenotypic characterization showed that the strain was bile- and acid-tolerant, attached to intestinal epithelial cells, and exhibited favorable cell surface properties and antimicrobial activity against key pathogens. It was susceptible to CLSI-recommended antibiotics and produced no cytotoxicity or enterotoxicity. Comparative genome analysis of L. plantarum 022AE revealed genetic determinants for survival in stress environments, cell adhesion, and virulence factor genes. Discussion Genomic analysis was instrumental in concluding the safety of L. plantarum 022AE. Integrated genetic and phenotypic analysis contributed in establishing the stability (in-vitro gut model, acid and bile), GI persistence (adherence to Caco2 and mucin and aggregation), functionalities ( βgalactosidase, Bile Salt hydrolase, anti-oxidants, anti-microbial substances) and capabilities (thermal and aqueous buffer stability) of L. plantarum 022AE indicating its suitability in human and animal nutrition. Conclusion The entire genome study and phenotypic evaluation exhibited a positive profile in terms of safety and probiotic attributes of L. plantarum 022AE, in alignment with current regulatory standards, suggesting its potential for use in applications requiring safe microbial strains, particularly in the food and pharmaceutical industries.